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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacagatataagattcctgccattgaataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
--------aacagatataagattcctgccattgaat--aacatatagtttttgtaca----agcttcatcaatattttc----accttacaagttacaaaa--------acaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
        | |    |||  ||     | ||  | |  || ||| ||   |    |     |  || ||| | |   ||    |  | | | |  |||| |        | ||| | || |||||||||||||||||||||||||||||||| ||||| ||||| ||||||||||| |||||| ||||  |||| |||| ||||||||||||||| ||||||||||
gtactaatatcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 2
--aacagatataagattcctgc-cattgaataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
  || |   | | | |   | | | ||  ||   |||||  | |  |    |   |||   | | |  ||     || ||         || |  | |||||||| |||||||| ||||||||  |||| ||||| ||||| || |||||| | |||||||| ||  | ||||| | | | ||||||||||| |||||||| |
ataatattgacagggtgttttcactttccatggaatatatatatatttttggtagcattgctttgtgtact---aaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 3
aacagatataagattcctgccattgaataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
|    ||||        ||   |    |  | |  | | | | ||        | || |  |||        || ||         || |  | |||||||| |||||||| ||||||||  |||| ||||| ||||| || |||||| | |||||||| ||  | ||||| | | | ||||||||||| |||||||| |
atataatattgagcgggtgttttcactttccgtggaatatatatattttgggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G15320.1 (Glycine max), 3'ss of exon 3
-------------aacagat---ataagattcctgccattga-ataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
             ||  |     ||   |||| |  | |||| |||  |  || |   | || |   |  || || ||  | |    | | ||       | ||  | || |||||||| |||||||||||| |||| ||||| ||||| |||||||| |||||| | |||||||| ||  ||||| | ||| | ||||||||||| |||||||| |
gtacaattcagtcaattgtcctgatggcattcttttctttgatatactaccta-taaatatatata-tggatgaaaatactgatgagataggtctagctcataa-attattttgcagGGAATGTTTGTTCCTACTATCAAAGGACAAGGAACTGAGGAACAGCAGCAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGCTATGCCC

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 3
-------------aacagat---ataagattcctgccattga-ataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
             ||  |     ||   |||| |  | |||| |||  |  ||       || |   || || || ||  |||    | | ||       | ||  |  | |||||||| ||||||||||||||||| ||||| ||||| |||||||| |||||||| |||||||| ||  ||||| | ||| | ||||||||||| || ||||| |
gtacaattcagttaattgtcctgatggcattcttttctttgatatattacctaaaaag-atatata-ttgatgaaaatactcatgagataggtctagctcataa-attcttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 3
aacagatataagattcctgccattgaataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
              | || ||  ||  |  ||| ||  || || | |       |  ||  ||| |         ||        |         |  |||| |||||||| |||||||| || || || ||||| |||||||||||||| ||||||||  |  ||||  | ||| | || || |||||||| ||||| |
-------------gtactacc--tgcgtctcatttatcttctggagacaggattttgattctttgattc-----attgtttttgtatctctgctctatagGGAATGTTTGTGCCTGCTATTAAGGGGCAGGGTACAGAGGAGCAGCAGAAGAAGTGGTTGTCGCTGGCCAATAAGATGCAGATTATTGGGTGTTATGCAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|78109870|gb|DV528286.1|DV528286
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|78092061|gb|DV520435.1|DV520435
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|18963249|gb|BM660327.1|BM660327
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|101399209|gb|EB821478.1|EB821478
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|78118216|gb|DV536603.1|DV536603
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|31558694|gb|CD527906.1|CD527906
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|71438097|gb|DR819147.1|DR819147
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|31557927|gb|CD527139.1|CD527139
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|149044450|gb|EE047571.2|EE047571
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|18655284|gb|BM500089.1|BM500089
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|148952746|gb|EC898728.2|EC898728
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|149089538|gb|EE178785.2|EE178785
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|149096635|gb|EE182400.2|EE182400
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|211287634|gb|FL366210.1|FL366210
EST:     GTATGCTGAGGCTATATGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|148942481|gb|EC887498.2|EC887498
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|71315288|gb|DR794256.1|DR794256
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|148974786|gb|EE025606.2|EE025606
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
EST: gi|149106570|gb|EE188463.2|EE188463
EST:     GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGG                         GGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA
genomic: GTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

AGGAGGAAGCAGGTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 442

AGGAGGAAGCAGGTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 403

AGGAGGAAGCAGGTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 701

AGGAGGAAGCAGGTATGCTGAGGCTATACGTCGATCAGCCTGGTTATGTTGATCTGCATTGGgtatgcctat ... catcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
                    accttac  putative branch site (score: 701)
                                            tcatctt  putative PPT
     ttcatcaatatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacagatataagattcctgccattgaataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC

- - - - - - - tcctgcc
- - - - - - - - - - - - -aataaca
- - - - - - - - - - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - -cttcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaca